The Geocore Industry has a start date of 1800, which is why it pops up so early. The developers obviously intended for it just to be used in the campaigns, or to be manually placed down in specific locations. Unfortunately, you can't change the start date of industry in-game without editing the exe file.
I have a nice easy solution that is slightly cheating but it does solve the problem. Use the cheat Casey Jones every 25 years, or when you see this is happening. The AI's trains will die, and they should get new ones that don't replace. Of Course it is cheating, but there isn't much else you can do without editing the hex codes. Maybe that cheat code was purely designed for this problem. CASEY JONES